Islamabad, Pakistan – The confrontation between the civilian government and the army in Pakistan turned into a bitter open clash Wednesday, when the military warned that remarks this week by the prime minister had “potentially grievous consequences for the country.”

It is thought that the military is maneuvering to remove the president, Asif Zardari, by using the courts. But his determination to hang on could result in another coup, analysts believe. There is speculation that, to head off the military’s plan, the government will try to sack the army chief.

Convulsed by the political crisis, nuclear-armed U.S. ally Pakistan is not focused on the pressing security and economic issues that concern Washington. Pakistan’s help is considered crucial to stabilizing Afghanistan and pushing for peace talks.

The military and the government are at loggerheads over a scandal dubbed “memogate,” in which the former ambassador to Washington is accused of making a “treacherous” written offer to the United States, to rein in Pakistan’s military, in return for American support for the civilian government. The case, aimed squarely against Zardari, is before the Supreme Court, which appointed a judicial commission that began hearings this week.

The prime minister, Yousaf Raza Gilani, had this week dubbed the affidavits to the court of the army chief and the head of the military’s spy agency as “unconstitutional and illegal.”

The military, in a highly unusual statement, responded Wednesday, saying that “there can be no allegation more serious” leveled against the army chief, Gen Ashfaq Kayani and the director general of Inter-Services Intelligence (ISI), Lt Gen Ahmed Shuja Pasha.

“This has very serious ramifications with potentially grievous consequences for the country,” the military’s statement said.

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In their court written testimonies, Kayani and Pasha had pressed the judges to investigate the allegations against the former U.S. envoy, Husain Haqqani, while the government had asked the court to drop the case and leave it to an investigation by a parliamentary committee. The government was shocked that the military’s affidavits had not been cleared by it first, though technically they were filed through the government’s attorney general.

In his affadavit, Pasha said that he had “seen enough corroborative material” to “prove” the allegations against the Washington ambassador, who was forced to resign over the issue.

The military insisted in its statement Wednesday that it had “followed the book” in responding to the court proceedings.

Also Wednesday, the government removed the retired general who was the top bureaucrat in the defense ministry, and replaced him with a loyalist to the ruling Pakistan Peoples Party. That fueled rumors that the government is considering changing the military’s leadership, an authority that it legally possesses but would be a highly risky move.

The army reportedly called a meeting of senior commanders for Thursday. The army has staged four coups in the past and democracy was only restored by elections in 2008 from the latest period of military rule. The military and Zardari’s government have been in a state of near constant tension since the 2008 polls. In particular, the military considers the government as too close to the United States.

In a move that heightened speculation of a military intervention, it emerged that the commander of the famous 111th Brigade, the army unit based in Rawalpindi that is used to stage coups, had been changed. The military said it was a “routine” change in command, which took place Wednesday.

The memogate furor depends on the allegations of an American businessman, Mansoor Ijaz, who in May had delivered the missive – supposedly dictated by the U.S. ambassador on behalf of Zardari – to the then Chairman of the U.S. Joint Chiefs of Staff, Admiral Mike Mullen. The existence of the anonymous memo came to light in October when Ijaz wrote about it, kicking off the scandal.

The case could yet lead to treason charges being filed against Haqqani, who said in an interview with McClatchy this week that he was the victim of a “witch-hunt” against democracy in the country. Ijaz is due to fly into Pakistan next week to testify before a judicial commission now probing the issue.

Attempting to cool tempers, a senior government minister, Khursheed Shah, said Wednesday that change was not afoot.

“The army chief will complete his tenure. We don’t want a clash of institutions,” said Shah.

Memogate is just one of the legal challenges that the government faces. Tuesday, in a separate constitutional case, the Supreme Court had ordered the government to revive a corruption probe against Zardari, related to alleged money laundering in Switzerland dating back to the 1990s.

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